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Ancestral BG1 Alleles and Structural Conservation Ensure Immune-Related Genetic Resilience in Southeast Asian Chicken Lineages
(2026-05-01)
Luu, Anh Huynh
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Budi, Trifan
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Singchat, Worapong
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Nguyen, Chien Tran Phuoc
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Panthum, Thitipong
Chicken (Gallus gallus domesticus) domestication, likely associated with dry-rice farming in central Thailand, has led to substantial loss of ancestral immune-related genetic diversity in commercial chicken lineages. This study addresses allelic loss by providing the first comprehensive analysis of the highly polymorphic BG1 gene, an MHC-linked marker across the wild–domestic interface in Thailand and Vietnam, using high-depth Illumina amplicon sequencing. Genomic DNA from 47 Thai and Vietnamese chicken populations was extracted using a salting-out protocol following ethical sampling. Allelic variation was examined by targeting the BG1 intron 15–exon 16 region using triplicate PCR and Salus Pro NGS sequencing. Evolutionary dynamics and selection pressures were analyzed using AmpliSAS, MrBayes, and Datamonkey, while AlphaFold 3 was used to predict and validate 3D protein structures. We identified 98 novel alleles and 172 polymorphic sites within the BG1 intron 15–exon 16 region encoding an Ig-like domain. Extensive allele sharing between indigenous chickens and red junglefowl indicated strong balancing selection and trans-species polymorphism. Selection analyses showed that purifying selection conserved structural integrity at codons 9, 13, and 18, while variation at other sites enhanced immune recognition. AlphaFold 3 modeling confirmed conservation of the β-sandwich fold across variants, maintaining stability of the Immunoreceptor Tyrosine-based Inhibition Motif (ITIM). Thus, despite the regional gene flow, geographic isolation has shaped distinct signatures, as evidenced by the presence of 38 unique Thai and 9 unique Vietnamese alleles in addition to breed-specific private markers in the Betong (BG1*TH88), Decoy (BG1*TH91), and Tre (BG1*VN54) populations. A notable adaptive outlier under positive selection (ω = 1.357) was detected in the Dong Tao population, suggesting a recent selective sweep. These findings support the mission of the Siam Chicken Bioresource Project (SCBP) to utilize indigenous breeds as genetic reservoirs and provide a molecular basis for restoring resilience traits in domestic poultry to enhance global food security.
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Saving the Mahachai Betta: Genetic Erosion and Conservation Priorities Under Urbanization Pressure
(2025-10-01)
Nguyen, Ton Huu Duc
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Budi, Trifan
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Pongsanarm, Tavun
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Panthum, Thitipong
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Singchat, Worapong
Background/Objectives: Mahachai Betta (Betta mahachaiensis) is a bubble-nesting fighting fish endemic to brackish habitats in Bangkok, Samut Sakhon, and Samut Prakan, where rapid urbanization and industrial growth threaten persistence. We evaluated genetic structure and diversity across 10 populations (81 individuals) to inform conservation planning. Methods: This study combined microsatellite genotyping (13 loci) with ecological niche modeling to assess genetic variability, population connectivity, and landscape–environmental drivers of differentiation. Results: Habitat loss and fragmentation were associated with reduced gene flow and decreased genetic diversity. Mean allelic richness was 2.65 and expected heterozygosity ranged from 0.20 to 0.46, with F<inf>ST</inf> values up to 0.400. Forward simulations predicted severe erosion of diversity within the next 12.5–37.5 years. Populations showed clear genetic subdivision, most pronounced in Samut Prakan and Samut Sakhon, with two Samut Sakhon populations (SKN3 and SKN7) reflecting strong environmental heterogeneity. Conclusions: Improving habitat connectivity and intensifying local community engagement are priority actions to enhance the resilience and long-term persistence of Mahachai Betta. This study provides the first integrated genetic and landscape-based assessment of the species, highlighting its rapid genetic erosion under urbanization and offering a foundation for targeted, evidence-based conservation strategies.
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Genetic Diversity and Selection of MHC I-UAA in Clariid Catfish from Thailand: Implications for Breeding and Conservation
(2025-09-01)
Nguyen, Ton Huu Duc
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Chalermwong, Piangjai
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Patta, Chananya
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Jaito, Wattanawan
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Singchat, Worapong
Background/Objectives: Understanding variabilities in the Major Histocompatibility Complex class I (MHC I) gene is essential for evaluating immunogenetic diversity in clariid catfish. MHC I plays a critical role in immune defense by presenting endogenous antigens to cytotoxic T cells. Therefore, we aimed to investigate the genetic diversity, selection patterns, and phylogenetic relationships of MHC I alleles in three important clariid catfish species (Clarias gariepinus, Clarias macrocephalus, and Clarias batrachus) across wild and hatchery populations in Thailand. Methods: Targeted next-generation sequencing of a 174 bp fragment partial exon 6 of MHC I-UAA gene was performed, along with phylogenetic analyses, neutrality tests and dN/dS analyses. Results: Overall, 91 novel alleles were identified in 674 individuals, all of which were novel (100% novelty), with none matching existing reference sequences, thereby revealing extensive variation in population-specific variants. Phylogenetic analyses revealed allele sharing among species, which was consistent with balanced selection. Neutrality tests and dN/dS analyses provided evidence of both purifying and diversifying selection, with episodic positive selection detected at multiple codon sites associated with the antigen-binding α1 domain. Distinct selection patterns among populations, influenced by local environmental conditions and human pressures, along with high allele richness, are reflected in the diversity of immunogenetic variations. Conclusions: These findings provide critical insights into immune adaptation and highlight the potential of MHC I as a functional marker for genetic monitoring. Although a causal relationship between MHC I polymorphism and disease resistance is debated, studies suggest associations with pathogen survival, indicating future implications for aquaculture breeding and conservation, particularly in marker-assisted selection for broodstock management in Thailand.

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